Theme A: Specification of Macroscopic Pattern Theme Leader: Lander. Other Project Faculty: Marsh, Nie, Schilling, Wan, Warrior, Xin, Yu Much of the macroscopic patterning of tissues is orchestrated by gradients of extracellular signaling molecules known as morphogens, which act during embryonic stages over distances of many tens of micrometers, to influence cell fates in a spatiallydependent manner. Morphogen gradients position boundaries of gene expression that define the locations of germ layers, body segments, and many tissue elements. In recent years, much has been learned about the identities of morphogens, and the receptors and signaling pathways used by cells to detect them (Neumann and Cohen, 1997;Tickle, 1999;Green, 2002;Tabata and Takei, 2004;Ashe and Briscoe, 2006). Morphogen gradients have long intrigued mathematicians and physicists because the problem of creating complex forms de novo (or from simpler forms) is mathematically interesting, and has general applicability to both physical and biological systems. Indeed, mathematicians (such as Turing, and Gierer) and engineers (Wolpert) developed a whole field of theoretical morphogen gradient study (Murray, 1993) long before biologists were willing to agree that morphogens even exist. As the study of morphogen gradients has increasingly moved into the hands of experimentalists, it has emerged that most morphogen gradient systems are far more complex than had been expected. Signs of complex control circuitry[unreadable]feedback loops, secreted inhibitors, coreceptors, regulation of diffusivity, cooperative interactions among morphogens[unreadable]abound, implying that morphogen gradients are constructed to do far more complex things than theoreticians had anticipated (Lander, 2007). What are the "missing" performance objectives of morphogen gradients? This question has come to dominate much of the experimental and theoretical work in the field. Some investigators have focused on questions of morphogen transport: Is simple diffusion adequate to create useful gradients? Does experimental evidence support the existence of active transport mechanisms that supplement or replace diffusion? Why are some morphogens covalently modified with cholesterol or fatty acids, which should make them less diffusible? Other investigators have focused on questions of robustness, i.e. the insensitivity of patterning to genetic or environmental perturbation. This is a rich area for investigation because experiments show that many patterning systems are extraordinarily robust, far more so than predicted by "classical" morphogen models. A recent assessment suggests that the performance objectives of morphpogen gradient systems go even deeper than just providing for insensitivity to environmental and genetic change (Lander, 2007). Some such systems appear to be under difficult time constraints;others may need to suppress internal noise (see below);in some cases different classes of morphogens may work together to overcome each other's inherent limitations (White et al., 2006). Clearly there is a great deal to be learned about what morphogen gradient systems are doing, and what strategies they exploit to do it. This area provides especially fertile ground for model exploration, and several good examples of large-scale parameter space exploration have come from this field (e.g. von Dassow et al., 2000;Eldar et al., 2002;Eldar et al., 2003;Ingolia, 2004). Efforts have also progressed toward building detailed mechanistic models for validation (Goentoro et al., 2006;Reeves et al., 2006), although it is clear that barriers to measuring key parameters such as levels of morphogens and receptors, and rate constants of production, interaction and destruction, need to be reduced.